What kind of pedals did you get? They should not be that hard to get into!
I sometimes have a little trouble clipping in with my second foot with my Eggbeater Candies, but I think that's mostly because of the uneven-ness of the trail. It's hard to coast long enough to get clipped in. I never seem to get my foot in the right place, or it takes longer than it does on my road bike. I clip in just fine with the first foot.
A friend recommended Speedplay Frogs, saying they are SUPER easy to clip into. If it's not too late, maybe you can exchange your pedals and try Frogs instead? They also offer a ton of float, which might help with the knee pain you're having.
Good luck!
Emily
Emily
2011 Jamis Dakar XC "Toto" - Selle Italia Ldy Gel Flow
2007 Trek Pilot 5.0 WSD "Gloria" - Selle Italia Diva Gel Flow
2004 Bike Friday Petite Pocket Crusoe - Selle Italia Diva Gel Flow